AutoCloner

Multiple sequence alignment - TraesCS1B01G269300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G269300	chr1B	100.000	2276	0	0	1	2276	473558153	473555878	0.000000e+00	4204
1	TraesCS1B01G269300	chr5B	93.942	1304	77	2	1	1302	540319753	540321056	0.000000e+00	1969
2	TraesCS1B01G269300	chr5B	86.708	1294	164	7	3	1291	503775921	503777211	0.000000e+00	1430
3	TraesCS1B01G269300	chr7D	92.337	1305	95	4	1	1303	535846422	535847723	0.000000e+00	1851
4	TraesCS1B01G269300	chr1D	92.361	1309	82	5	1	1307	479322488	479321196	0.000000e+00	1847
5	TraesCS1B01G269300	chr1D	91.006	934	46	13	1304	2216	351108822	351107906	0.000000e+00	1225
6	TraesCS1B01G269300	chr1D	89.367	395	20	4	1896	2276	350948914	350948528	5.690000e-131	477
7	TraesCS1B01G269300	chr3D	90.261	1304	122	5	1	1301	44971318	44972619	0.000000e+00	1700
8	TraesCS1B01G269300	chr3D	85.429	1304	185	5	1	1302	284850700	284849400	0.000000e+00	1351
9	TraesCS1B01G269300	chr6A	88.872	1303	144	1	1	1302	13040047	13041349	0.000000e+00	1602
10	TraesCS1B01G269300	chr6B	87.117	1304	160	7	1	1302	63785034	63786331	0.000000e+00	1471
11	TraesCS1B01G269300	chr7B	85.056	1258	182	6	51	1304	443324643	443325898	0.000000e+00	1277
12	TraesCS1B01G269300	chr3B	81.860	1312	226	10	1	1305	816086585	816087891	0.000000e+00	1094
13	TraesCS1B01G269300	chr1A	90.394	812	38	13	1489	2276	451853368	451852573	0.000000e+00	1031
14	TraesCS1B01G269300	chr1A	94.702	151	7	1	1304	1454	451853516	451853367	1.360000e-57	233

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G269300	chr1B	473555878	473558153	2275	True	4204	4204	100.000	1	2276	1	chr1B.!!$R1	2275
1	TraesCS1B01G269300	chr5B	540319753	540321056	1303	False	1969	1969	93.942	1	1302	1	chr5B.!!$F2	1301
2	TraesCS1B01G269300	chr5B	503775921	503777211	1290	False	1430	1430	86.708	3	1291	1	chr5B.!!$F1	1288
3	TraesCS1B01G269300	chr7D	535846422	535847723	1301	False	1851	1851	92.337	1	1303	1	chr7D.!!$F1	1302
4	TraesCS1B01G269300	chr1D	479321196	479322488	1292	True	1847	1847	92.361	1	1307	1	chr1D.!!$R3	1306
5	TraesCS1B01G269300	chr1D	351107906	351108822	916	True	1225	1225	91.006	1304	2216	1	chr1D.!!$R2	912
6	TraesCS1B01G269300	chr3D	44971318	44972619	1301	False	1700	1700	90.261	1	1301	1	chr3D.!!$F1	1300
7	TraesCS1B01G269300	chr3D	284849400	284850700	1300	True	1351	1351	85.429	1	1302	1	chr3D.!!$R1	1301
8	TraesCS1B01G269300	chr6A	13040047	13041349	1302	False	1602	1602	88.872	1	1302	1	chr6A.!!$F1	1301
9	TraesCS1B01G269300	chr6B	63785034	63786331	1297	False	1471	1471	87.117	1	1302	1	chr6B.!!$F1	1301
10	TraesCS1B01G269300	chr7B	443324643	443325898	1255	False	1277	1277	85.056	51	1304	1	chr7B.!!$F1	1253
11	TraesCS1B01G269300	chr3B	816086585	816087891	1306	False	1094	1094	81.860	1	1305	1	chr3B.!!$F1	1304
12	TraesCS1B01G269300	chr1A	451852573	451853516	943	True	632	1031	92.548	1304	2276	2	chr1A.!!$R1	972

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
139	140	0.106868	TCATTGCCCCAGATGCTGAG	60.107	55.0	0.0	0.0	32.44	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1354	1364	0.03601	CTCCTGCCCACCTTACACTG	60.036	60.0	0.0	0.0	0.0	3.66	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	115	3.645212	TGGAAGCAGGATCTGATTAGGAG	59.355	47.826	0.00	0.00	40.30	3.69
139	140	0.106868	TCATTGCCCCAGATGCTGAG	60.107	55.000	0.00	0.00	32.44	3.35
156	157	4.164030	TGCTGAGGCTATTCTTAACATCCA	59.836	41.667	0.00	0.00	39.59	3.41
158	159	5.767168	GCTGAGGCTATTCTTAACATCCAAT	59.233	40.000	0.00	0.00	35.22	3.16
170	173	4.402616	AACATCCAATTCAGAAGGGGAA	57.597	40.909	9.11	0.00	0.00	3.97
200	203	4.079212	AGGATTTCTATGCTTGGGCCTTTA	60.079	41.667	4.53	0.00	37.74	1.85
300	303	2.978824	GGCTACCGGTGCTTCTCA	59.021	61.111	19.93	0.00	0.00	3.27
331	334	1.003839	GATGTGGACGGCCTTGTGA	60.004	57.895	9.82	0.00	34.31	3.58
649	654	1.875009	CATCATGTGGACGATCTGGG	58.125	55.000	0.00	0.00	0.00	4.45
831	837	0.238289	CAACGGATGGTGCACTCAAC	59.762	55.000	17.98	11.39	0.00	3.18
896	902	1.587613	CAGCGCTACTCGGAGCTTC	60.588	63.158	10.99	0.00	40.15	3.86
1011	1018	3.668447	GCATGTGATAATGGAGACCGAT	58.332	45.455	0.00	0.00	0.00	4.18
1013	1020	5.237815	GCATGTGATAATGGAGACCGATTA	58.762	41.667	0.00	0.00	0.00	1.75
1138	1146	5.627499	TGAGATTCAACATGTAAACAGGC	57.373	39.130	0.00	0.00	0.00	4.85
1199	1209	2.809446	CACTCTGAATGCGACCGATTA	58.191	47.619	0.00	0.00	0.00	1.75
1294	1304	0.393537	AAGCTCTCTGATTTGCCCGG	60.394	55.000	0.00	0.00	0.00	5.73
1354	1364	2.713770	TCGCCGTCGATCTACAGC	59.286	61.111	0.00	0.00	40.21	4.40
1409	1420	2.957006	GGAAACGGCTACTCCTCATCTA	59.043	50.000	0.00	0.00	0.00	1.98
1464	1475	4.768583	AGATTCTCAAGTCCTGATCAAGC	58.231	43.478	0.00	0.00	32.14	4.01
1482	1493	1.286260	CGATCAGCCCCGTAGCTAC	59.714	63.158	14.19	14.19	42.61	3.58
1484	1495	1.041437	GATCAGCCCCGTAGCTACTT	58.959	55.000	21.20	0.00	42.61	2.24
1512	1523	3.795877	ACAAGACCATTTGGCAAAGTTG	58.204	40.909	18.61	16.25	39.32	3.16
1602	1614	1.405933	CCATTCGTGAGATGCCAGTGA	60.406	52.381	0.00	0.00	41.60	3.41
1665	1677	1.576421	CGTGCCTTTCCTGCAAGAC	59.424	57.895	0.00	0.00	41.06	3.01
1673	1685	2.501223	TTCCTGCAAGACGTAGCCGG	62.501	60.000	0.00	0.00	38.78	6.13
1709	1721	2.310233	CCGTAGCATCGCAATCCCG	61.310	63.158	0.00	0.00	0.00	5.14
1728	1740	1.957765	GAGGCTCCCGTCCACCTTAC	61.958	65.000	2.15	0.00	30.95	2.34
1783	1795	7.464769	ACCTAAAATCCTTTTGGTCACGTACC	61.465	42.308	7.11	7.11	44.28	3.34
1854	1881	0.626916	AGCGGGGGCCTATTGTTAAA	59.373	50.000	0.84	0.00	0.00	1.52
1861	1888	3.450817	GGGGCCTATTGTTAAACTTGCAT	59.549	43.478	0.84	0.00	0.00	3.96
1918	1945	2.401766	GGCAACTGCATCCTCACGG	61.402	63.158	3.76	0.00	44.36	4.94
1998	2025	2.527951	CTAAAGCCAGAGCGCCCAGT	62.528	60.000	2.29	0.00	46.67	4.00
1999	2026	2.124507	TAAAGCCAGAGCGCCCAGTT	62.125	55.000	2.29	0.00	46.67	3.16
2000	2027	4.711949	AGCCAGAGCGCCCAGTTG	62.712	66.667	2.29	0.00	46.67	3.16
2002	2029	4.020617	CCAGAGCGCCCAGTTGGA	62.021	66.667	2.29	0.00	37.39	3.53
2003	2030	2.032528	CAGAGCGCCCAGTTGGAA	59.967	61.111	2.29	0.00	37.39	3.53
2004	2031	2.032681	AGAGCGCCCAGTTGGAAC	59.967	61.111	2.29	0.00	37.39	3.62
2035	2063	7.545489	AGAATTCCATTTCTCAGATCAAAAGC	58.455	34.615	0.65	0.00	29.99	3.51
2053	2086	4.748798	CTCCAGGACCAGGGCCCT	62.749	72.222	22.28	22.28	0.00	5.19
2057	2090	2.121506	AGGACCAGGGCCCTTTCA	60.122	61.111	26.10	0.00	0.00	2.69
2090	2123	0.593128	ATGAAACGCAGAGCAACCAC	59.407	50.000	0.00	0.00	0.00	4.16
2109	2142	2.096496	CACTTGGAGGAATTCGACATGC	59.904	50.000	0.00	0.00	0.00	4.06
2125	2158	5.046529	CGACATGCTAAAAGCTCTAGATGT	58.953	41.667	6.93	11.32	42.97	3.06
2148	2181	3.479269	CCGAACTTCCTGACGCGC	61.479	66.667	5.73	0.00	0.00	6.86
2169	2202	0.764890	AGGCCTCTTGTGTGCAGTTA	59.235	50.000	0.00	0.00	0.00	2.24
2178	2225	2.892374	TGTGTGCAGTTAGATGATCCG	58.108	47.619	0.00	0.00	0.00	4.18
2183	2230	1.262683	GCAGTTAGATGATCCGCTTGC	59.737	52.381	0.00	0.00	0.00	4.01
2248	2295	2.536761	TGGACGACCCAGTAAACAAG	57.463	50.000	0.34	0.00	40.82	3.16
2264	2311	5.993748	AAACAAGTTGGTTTTCTGGAGAA	57.006	34.783	7.96	0.00	37.72	2.87
2273	2320	4.943705	TGGTTTTCTGGAGAACATATCAGC	59.056	41.667	6.39	0.00	33.13	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	6.747414	AGCAAAGGTGACATAGATATGGTA	57.253	37.500	4.93	0.00	38.00	3.25
114	115	2.301346	CATCTGGGGCAATGAAGGTAC	58.699	52.381	0.00	0.00	0.00	3.34
139	140	7.807977	TCTGAATTGGATGTTAAGAATAGCC	57.192	36.000	0.00	0.00	0.00	3.93
156	157	3.779738	CTCTCCTCTTCCCCTTCTGAATT	59.220	47.826	0.00	0.00	0.00	2.17
158	159	2.560841	CCTCTCCTCTTCCCCTTCTGAA	60.561	54.545	0.00	0.00	0.00	3.02
170	173	4.347583	CCAAGCATAGAAATCCTCTCCTCT	59.652	45.833	0.00	0.00	35.41	3.69
200	203	3.067106	CAGTGTAGTTGCCTGATCGTTT	58.933	45.455	0.00	0.00	0.00	3.60
300	303	5.118990	CCGTCCACATCTGTTTATCATCTT	58.881	41.667	0.00	0.00	0.00	2.40
331	334	7.066525	TCGTACTTTGGAATCACTTTGAGTTTT	59.933	33.333	0.00	0.00	0.00	2.43
649	654	2.096516	GCTTGATCCGATTGCGAGAATC	60.097	50.000	0.00	0.00	40.82	2.52
700	706	2.108168	CTCCCTTGTCGACCTTATGGA	58.892	52.381	14.12	10.64	37.04	3.41
896	902	4.368808	CACCGAACGGCTTGCACG	62.369	66.667	13.32	0.00	39.32	5.34
972	979	3.446310	TGCGATATGCCTCGAAGTTTA	57.554	42.857	4.81	0.00	45.60	2.01
1322	1332	2.499685	CGACCCCGACATTCCTCC	59.500	66.667	0.00	0.00	38.22	4.30
1354	1364	0.036010	CTCCTGCCCACCTTACACTG	60.036	60.000	0.00	0.00	0.00	3.66
1409	1420	4.805609	GCTTTGAGAGAGACAAGTTGGGAT	60.806	45.833	7.96	0.00	0.00	3.85
1464	1475	1.173444	AGTAGCTACGGGGCTGATCG	61.173	60.000	17.99	0.00	43.01	3.69
1472	1483	0.813184	TCACGGAAAGTAGCTACGGG	59.187	55.000	17.99	7.41	0.00	5.28
1482	1493	3.304659	CCAAATGGTCTTGTCACGGAAAG	60.305	47.826	0.00	0.00	0.00	2.62
1484	1495	2.226330	CCAAATGGTCTTGTCACGGAA	58.774	47.619	0.00	0.00	0.00	4.30
1512	1523	2.692041	CAGGGATTCCAAAGCCAGAATC	59.308	50.000	4.80	4.52	44.99	2.52
1602	1614	1.203013	TCGGGTCAGGATATGGATCGT	60.203	52.381	0.00	0.00	32.28	3.73
1673	1685	2.879462	CCTACGGACGAGTTGCGC	60.879	66.667	0.00	0.00	44.28	6.09
1709	1721	1.684734	TAAGGTGGACGGGAGCCTC	60.685	63.158	0.00	0.00	0.00	4.70
1728	1740	1.290009	CAAGAAAGGGCGGCCAAAG	59.710	57.895	31.59	9.56	0.00	2.77
1783	1795	1.371758	CCTGACCGACACGACACAG	60.372	63.158	0.00	0.00	0.00	3.66
1784	1796	2.725641	CCTGACCGACACGACACA	59.274	61.111	0.00	0.00	0.00	3.72
1785	1797	2.733593	GCCTGACCGACACGACAC	60.734	66.667	0.00	0.00	0.00	3.67
1786	1798	4.337060	CGCCTGACCGACACGACA	62.337	66.667	0.00	0.00	0.00	4.35
1787	1799	4.338539	ACGCCTGACCGACACGAC	62.339	66.667	0.00	0.00	0.00	4.34
1819	1844	2.541588	CCCGCTTATCTTTCGCCAATTG	60.542	50.000	0.00	0.00	0.00	2.32
1827	1854	0.763035	TAGGCCCCCGCTTATCTTTC	59.237	55.000	0.00	0.00	34.44	2.62
1918	1945	8.421784	TGAACTTCTCATGACCCACTTATATAC	58.578	37.037	0.00	0.00	0.00	1.47
2090	2123	2.636830	AGCATGTCGAATTCCTCCAAG	58.363	47.619	0.00	0.00	0.00	3.61
2109	2142	8.325421	TCGGAGTATACATCTAGAGCTTTTAG	57.675	38.462	5.50	0.00	0.00	1.85
2125	2158	2.357009	GCGTCAGGAAGTTCGGAGTATA	59.643	50.000	0.00	0.00	0.00	1.47
2169	2202	2.775890	CTAATGGCAAGCGGATCATCT	58.224	47.619	0.00	0.00	0.00	2.90
2248	2295	6.623767	GCTGATATGTTCTCCAGAAAACCAAC	60.624	42.308	0.00	0.00	35.58	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.